Mercurial > repos > iuc > pygenometracks
view pyGenomeTracks.xml @ 10:a1abfa420d9d draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 5bd033a726b088eef3cf591da36ca1e9ba70d8c7"
| author | iuc |
|---|---|
| date | Sun, 13 Feb 2022 22:43:45 +0000 |
| parents | 2824d77cd8f8 |
| children | 7dd841a32245 |
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<tool id="pygenomeTracks" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>plot genomic data tracks</description> <macros> <token name="@BINARY@">pyGenomeTracks</token> <import>macros.xml</import> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"> <![CDATA[ ## First symlink data of hic to have the good extension #for $counter, $track in enumerate($tracks): #if $track.track_file_style_conditional.track_file_style_selector == "hic_matrix_option": #for $counter_matrix, $data_matrix in enumerate($track.track_file_style_conditional.matrix_h5_cooler_multiple): #set ext = $data_matrix.extension ln -s $data_matrix ${counter}_${counter_matrix}.$ext && #end for #end if #end for sed '/^$/d' '$tracks_config' && @BINARY@ --tracks '$tracks_config' --region '$region' #if $global_args.title != '': --title '$global_args.title' #end if #if $global_args.plotWidth != '': --plotWidth $global_args.plotWidth #else: --width $global_args.width #end if #if $global_args.height != '': --height '$global_args.height' #end if --fontSize $global_args.fontsize --dpi $global_args.dpi --trackLabelFraction $global_args.trackLabelFraction --trackLabelHAlign $global_args.trackLabelHAlign --outFileName plot.$image_file_format $global_args.decreasingXAxis && mv plot.$image_file_format plot ]]> </command> <configfiles> <configfile name="tracks_config"> ## Each track: #for $counter, $track in enumerate($tracks): ## Hi-C Track #if $track.track_file_style_conditional.track_file_style_selector == "hic_matrix_option": #for $counter_matrix, $data_matrix in enumerate($track.track_file_style_conditional.matrix_h5_cooler_multiple): [hic_section_${counter}_${counter_matrix}] #set ext = $data_matrix.extension file = ${counter}_${counter_matrix}.$ext file_type = hic_matrix #if $track.track_file_style_conditional.title: title = $track.track_file_style_conditional.title #else: title = $data_matrix.element_identifier #end if #if $track.track_file_style_conditional.depth: depth = $track.track_file_style_conditional.depth #end if #if $track.track_file_style_conditional.colormap: colormap = $track.track_file_style_conditional.colormap #end if #if $track.track_file_style_conditional.min_value != "": min_value = $track.track_file_style_conditional.min_value #end if #if $track.track_file_style_conditional.max_value != "": max_value = $track.track_file_style_conditional.max_value #end if transform = $track.track_file_style_conditional.transform #if $track.track_file_style_conditional.height_matrix != "": height = $track.track_file_style_conditional.height_matrix #end if #if $track.track_file_style_conditional.show_masked_bins: show_masked_bins = $track.track_file_style_conditional.show_masked_bins #end if #if $track.track_file_style_conditional.invert_orientation: orientation = inverted #end if #if $track.track_file_style_conditional.scale_factor: scale_factor = $track.track_file_style_conditional.scale_factor #end if rasterize = $track.track_file_style_conditional.rasterize ## If a boundary file is given a new section needs to be written: #if str($track.track_file_style_conditional.boundaries_file) != "None": #if len($track.track_file_style_conditional.boundaries_file)>$counter_matrix: #set boundary_file = $track.track_file_style_conditional.boundaries_file[$counter_matrix] #else: #set boundary_file = $track.track_file_style_conditional.boundaries_file[0] #end if [tads_${counter}_${counter_matrix}] file = $boundary_file file_type = domains border_color = black color = none overlay_previous = share-y #end if ## If spacer is asked a new section is created: #if $track.track_file_style_conditional.spacer_height != "": [spacer] height = $track.track_file_style_conditional.spacer_height #end if #end for #end if ## Chrom_state track #if $track.track_file_style_conditional.track_file_style_selector == "chrom_states_option": #for $data_bed in $track.track_file_style_conditional.track_input_bed: [chrom states_$counter] file = $data_bed #if $track.track_file_style_conditional.title: title = $track.track_file_style_conditional.title #else: title = $data_bed.element_identifier #end if #if $track.track_file_style_conditional.color_bed.color_bed_select == "bed_rgb": color = bed_rgb #elif $track.track_file_style_conditional.color_bed.color: color = $track.track_file_style_conditional.color_bed.color #end if #if $track.track_file_style_conditional.border_color_bed.border_color_bed_select == 'manually': border_color = $track.track_file_style_conditional.border_color_bed.color #else border_color = $track.track_file_style_conditional.border_color_bed.border_color_bed_select #end if display = collapsed #if $track.track_file_style_conditional.height_chrom: height = $track.track_file_style_conditional.height_chrom #end if line_width = $track.track_file_style_conditional.line_width file_type = bed ## If spacer is asked a new section is created: #if $track.track_file_style_conditional.spacer_height != "": [spacer] height = $track.track_file_style_conditional.spacer_height #end if #end for #end if ## Gene/gtf track #if $track.track_file_style_conditional.track_file_style_selector == "gene_track_option": #for $counter_bed, $data_bed in enumerate($track.track_file_style_conditional.track_input_bed): [genes_${counter}_${counter_bed}] #set ext = $data_bed.extension file = $data_bed #if $ext == 'gtf': prefered_name = $track.track_file_style_conditional.bed_style.bed_advanced.gtf.prefered_name merge_transcripts = $track.track_file_style_conditional.bed_style.bed_advanced.gtf.merge_transcripts #end if #if $track.track_file_style_conditional.title: title = $track.track_file_style_conditional.title #elif $track.track_file_style_conditional.overlay_select == 'no': title = $data_bed.element_identifier #end if #if $track.track_file_style_conditional.color_bed.color_bed_select == "bed_rgb": color = bed_rgb #elif $track.track_file_style_conditional.color_bed.color: color = $track.track_file_style_conditional.color_bed.color #end if #if $track.track_file_style_conditional.border_color_bed.border_color_bed_select == 'manually': border_color = $track.track_file_style_conditional.border_color_bed.color #else border_color = $track.track_file_style_conditional.border_color_bed.border_color_bed_select #end if style = $track.track_file_style_conditional.bed_style.bed_style_select #if $track.track_file_style_conditional.bed_style.bed_style_select == 'UCSC': arrow_interval = $track.track_file_style_conditional.bed_style.bed_advanced.arrow_interval #else: height_utr = $track.track_file_style_conditional.bed_style.bed_advanced.height_utr #if $track.track_file_style_conditional.bed_style.bed_advanced.color_utr.color_utr_select == 'manually': color_utr = $track.track_file_style_conditional.bed_style.bed_advanced.color_utr.color #elif $track.track_file_style_conditional.bed_style.bed_advanced.color_utr.color_utr_select == 'bed_rgb': color_utr = bed_rgb #else: #if $track.track_file_style_conditional.color_bed.color_bed_select == "bed_rgb": color_utr = bed_rgb #else: color_utr = $track.track_file_style_conditional.color_bed.color #end if #end if #if $track.track_file_style_conditional.bed_style.bed_style_select == 'tssarrow' and $track.track_file_style_conditional.bed_style.bed_advanced.arrow_length != '': arrow_length = $track.track_file_style_conditional.bed_style.bed_advanced.arrow_length #end if #if $track.track_file_style_conditional.bed_style.bed_style_select == 'flybase': arrowhead_included = $track.track_file_style_conditional.bed_style.arrowhead_included #end if #end if display = $track.track_file_style_conditional.display #if $track.track_file_style_conditional.height_bed: height = $track.track_file_style_conditional.height_bed #end if labels = $track.track_file_style_conditional.labels.plot_labels #if $track.track_file_style_conditional.labels.plot_labels == 'true': all_labels_inside = $track.track_file_style_conditional.labels.all_labels_inside labels_in_margin = $track.track_file_style_conditional.labels.labels_in_margin #end if file_type = $ext #if $track.track_file_style_conditional.fontsize: fontsize = $track.track_file_style_conditional.fontsize #end if #if $track.track_file_style_conditional.bed_style.bed_advanced.gene_rows: gene_rows = $track.track_file_style_conditional.bed_style.bed_advanced.gene_rows #end if global_max_row = $track.track_file_style_conditional.bed_style.bed_advanced.global_max_row max_labels = $track.track_file_style_conditional.bed_style.bed_advanced.max_labels line_width = $track.track_file_style_conditional.bed_style.bed_advanced.line_width #if $track.track_file_style_conditional.invert_orientation: orientation = inverted #end if overlay_previous = $track.track_file_style_conditional.overlay_select ## If spacer is asked a new section is created: #if $track.track_file_style_conditional.spacer_height != "": [spacer] height = $track.track_file_style_conditional.spacer_height #end if #end for #end if ## Link #if $track.track_file_style_conditional.track_file_style_selector == "link_track_option": [links_$counter] file = $track.track_file_style_conditional.track_input_link #if $track.track_file_style_conditional.title: title = $track.track_file_style_conditional.title #elif $track.track_file_style_conditional.overlay_select == 'no': title = $track.track_file_style_conditional.track_input_link.element_identifier #end if #if $track.track_file_style_conditional.height: height = $track.track_file_style_conditional.height #end if #if $track.track_file_style_conditional.min_value != "": min_value = $track.track_file_style_conditional.min_value #end if #if $track.track_file_style_conditional.max_value != "": max_value = $track.track_file_style_conditional.max_value #end if color = $track.track_file_style_conditional.color_link.color alpha = $track.track_file_style_conditional.alpha line_width = $track.track_file_style_conditional.line_width line_style = $track.track_file_style_conditional.line_style links_type = $track.track_file_style_conditional.links_type compact_arcs_level = $track.track_file_style_conditional.compact_arcs_level #if $track.track_file_style_conditional.ylim != "": ylim = $track.track_file_style_conditional.ylim #end if use_middle = $track.track_file_style_conditional.use_middle #if $track.track_file_style_conditional.invert_orientation: orientation = inverted #end if overlay_previous = $track.track_file_style_conditional.overlay_select file_type = links ## If spacer is asked a new section is created: #if $track.track_file_style_conditional.spacer_height != "": [spacer] height = $track.track_file_style_conditional.spacer_height #end if #end if ## Narrow peak #if $track.track_file_style_conditional.track_file_style_selector == "narrow_peak_track_option": #for $counter_narrow_peak, $data_narrow_peak in enumerate($track.track_file_style_conditional.track_input_narrow_peak): [narrow_peak_${counter}_${counter_narrow_peak}] file = $data_narrow_peak #if $track.track_file_style_conditional.title: title = $track.track_file_style_conditional.title #elif $track.track_file_style_conditional.overlay_select == 'no': title = $data_narrow_peak.element_identifier #end if color = $track.track_file_style_conditional.color type = $track.track_file_style_conditional.display.display_selector use_summit = $track.track_file_style_conditional.display.use_summit #if $track.track_file_style_conditional.display.display_selector == "peak": show_data_range = $track.track_file_style_conditional.display.show_data #if $track.track_file_style_conditional.display.width_adjust: width_adjust = $track.track_file_style_conditional.display.width_adjust #end if #if $track.track_file_style_conditional.display.min_value != "": min_value = $track.track_file_style_conditional.display.min_value #end if #if $track.track_file_style_conditional.display.max_value != "": max_value = $track.track_file_style_conditional.display.max_value #end if #end if #if $track.track_file_style_conditional.height_narrow_peak: height = $track.track_file_style_conditional.height_narrow_peak #end if line_width = $track.track_file_style_conditional.line_width show_labels = $track.track_file_style_conditional.show_labels file_type = narrow_peak #if $track.track_file_style_conditional.fontsize: fontsize = $track.track_file_style_conditional.fontsize #end if #if $track.track_file_style_conditional.invert_orientation: orientation = inverted #end if overlay_previous = $track.track_file_style_conditional.overlay_select ## If spacer is asked a new section is created: #if $track.track_file_style_conditional.spacer_height != "": [spacer] height = $track.track_file_style_conditional.spacer_height #end if #end for #end if ## Bedgraph track #if $track.track_file_style_conditional.track_file_style_selector == "bedgraph_track_option": #for $data_bedgraph in $track.track_file_style_conditional.track_input_bedgraph: [bedgraph_$counter] file = $data_bedgraph #if $track.track_file_style_conditional.title: title = $track.track_file_style_conditional.title #elif $track.track_file_style_conditional.overlay_select == "no": title = $data_bedgraph.element_identifier #end if #if $track.track_file_style_conditional.color: color = $track.track_file_style_conditional.color #end if alpha = $track.track_file_style_conditional.alpha #if $track.track_file_style_conditional.color_negative.color_negative_select == "true": negative_color = $track.track_file_style_conditional.color_negative.color #end if #if $track.track_file_style_conditional.height_bedgraph: height = $track.track_file_style_conditional.height_bedgraph #end if #if $track.track_file_style_conditional.min_value != "": min_value = $track.track_file_style_conditional.min_value #end if #if $track.track_file_style_conditional.max_value != "": max_value = $track.track_file_style_conditional.max_value #end if show_data_range = $track.track_file_style_conditional.show_data grid = $track.track_file_style_conditional.grid nans_to_zeros = $track.track_file_style_conditional.nans_to_zeros use_middle = $track.track_file_style_conditional.use_middle #set $columns = len(open(str($track.track_file_style_conditional.track_input_bedgraph)).readline().split('\t')) #if $columns > 4: file_type = bedgraph_matrix type = lines #else: file_type = bedgraph #if $track.track_file_style_conditional.type_conditional.type_selector == 'fill_option': type = fill #elif $track.track_file_style_conditional.type_conditional.type_selector == 'line_option': type = line:$track.track_file_style_conditional.type_conditional.width_line #elif $track.track_file_style_conditional.type_conditional.type_selector == 'point_option': type = points:$track.track_file_style_conditional.type_conditional.width_point #end if #if $track.track_file_style_conditional.logScale_conditional.transform_selector != 'no': transform = $track.track_file_style_conditional.logScale_conditional.transform_selector y_axis_values = $track.track_file_style_conditional.logScale_conditional.y_axis_values #if $track.track_file_style_conditional.logScale_conditional.transform_selector != 'log1p': log_pseudocount = $track.track_file_style_conditional.logScale_conditional.log_pseudocount #end if #end if #end if #if $track.track_file_style_conditional.reading_bdg_as_bw.summary_method != 'no': summary_method = $track.track_file_style_conditional.reading_bdg_as_bw.summary_method #if $track.track_file_style_conditional.reading_bdg_as_bw.number_of_bins: number_of_bins = $track.track_file_style_conditional.reading_bdg_as_bw.number_of_bins #end if #end if #if $track.track_file_style_conditional.op.operation != 'file': operation = $track.track_file_style_conditional.op.operation #if 'second_file' in str($track.track_file_style_conditional.op.operation): second_file = $track.track_file_style_conditional.op.second_file #end if #end if #if $track.track_file_style_conditional.invert_orientation: orientation = inverted #end if overlay_previous = $track.track_file_style_conditional.overlay_select ## If spacer is asked a new section is created: #if $track.track_file_style_conditional.spacer_height != "": [spacer] height = $track.track_file_style_conditional.spacer_height #end if #end for #end if ## Bigwig tracks #if $track.track_file_style_conditional.track_file_style_selector == "bigwig_track_option": #for $data_bigwig in $track.track_file_style_conditional.track_input_bigwig: [bigwig_$counter] file = $data_bigwig #if $track.track_file_style_conditional.title: title = $track.track_file_style_conditional.title #elif $track.track_file_style_conditional.overlay_select == "no": title = $data_bigwig.element_identifier #end if #if $track.track_file_style_conditional.color: color = $track.track_file_style_conditional.color #end if alpha = $track.track_file_style_conditional.alpha #if $track.track_file_style_conditional.color_negative.color_negative_select == "true": negative_color = $track.track_file_style_conditional.color_negative.color #end if #if $track.track_file_style_conditional.min_value != "": min_value = $track.track_file_style_conditional.min_value #end if #if $track.track_file_style_conditional.max_value != "": max_value = $track.track_file_style_conditional.max_value #end if height = $track.track_file_style_conditional.height_bigwig summary_method = $track.track_file_style_conditional.reading_bw_conditional.summary_method nans_to_zeros = $track.track_file_style_conditional.reading_bw_conditional.nans_to_zeros #if $track.track_file_style_conditional.reading_bw_conditional.number_of_bins: number_of_bins = $track.track_file_style_conditional.reading_bw_conditional.number_of_bins #end if #if $track.track_file_style_conditional.type_conditional.type_selector == 'fill_option': type = fill #elif $track.track_file_style_conditional.type_conditional.type_selector == 'line_option': type = line:$track.track_file_style_conditional.type_conditional.width_line #elif $track.track_file_style_conditional.type_conditional.type_selector == 'point_option': type = points:$track.track_file_style_conditional.type_conditional.width_point #end if #if $track.track_file_style_conditional.logScale_conditional.transform_selector != 'no': transform = $track.track_file_style_conditional.logScale_conditional.transform_selector y_axis_values = $track.track_file_style_conditional.logScale_conditional.y_axis_values #if $track.track_file_style_conditional.logScale_conditional.transform_selector != 'log1p': log_pseudocount = $track.track_file_style_conditional.logScale_conditional.log_pseudocount #end if #end if #if $track.track_file_style_conditional.op.operation != 'file': operation = $track.track_file_style_conditional.op.operation #if 'second_file' in $track.track_file_style_conditional.op.operation: second_file = $track.track_file_style_conditional.op.second_file #end if #end if show_data_range = $track.track_file_style_conditional.show_data grid = $track.track_file_style_conditional.grid file_type = bigwig #if $track.track_file_style_conditional.invert_orientation: orientation = inverted #end if overlay_previous = $track.track_file_style_conditional.overlay_select ## If spacer is asked a new section is created: #if $track.track_file_style_conditional.spacer_height != "": [spacer] height = $track.track_file_style_conditional.spacer_height #end if #end for #end if ## bedgraph_matrix #if $track.track_file_style_conditional.track_file_style_selector == "bedgraph_matrix_track_option": #for $data_bedgraph_matrix in $track.track_file_style_conditional.track_input_bedgraph_matrix: [bedgraph_matrix_$counter] file = $data_bedgraph_matrix #if $track.track_file_style_conditional.title: title = $track.track_file_style_conditional.title #else: title = $data_bedgraph_matrix.element_identifier #end if #if $track.track_file_style_conditional.height_bedgraph: height = $track.track_file_style_conditional.height_bedgraph #end if #if $track.track_file_style_conditional.min_value != "": min_value = $track.track_file_style_conditional.min_value #end if #if $track.track_file_style_conditional.max_value != "": max_value = $track.track_file_style_conditional.max_value #end if type = $track.track_file_style_conditional.type.type_selector file_type = bedgraph_matrix #if $track.track_file_style_conditional.type.type_selector == 'lines': show_data_range = $track.track_file_style_conditional.type.show_data plot_horizontal_lines = $track.track_file_style_conditional.type.plot_horizontal_lines pos_score_in_bin = $track.track_file_style_conditional.type.pos_score_in_bin #else colormap = $track.track_file_style_conditional.type.colormap #end if #if $track.track_file_style_conditional.invert_orientation: orientation = inverted #end if ## If spacer is asked a new section is created: #if $track.track_file_style_conditional.spacer_height != "": [spacer] height = $track.track_file_style_conditional.spacer_height #end if #end for #end if ## Vlines: #if $track.track_file_style_conditional.track_file_style_selector == "vlines_track_option": [vlines_$counter] file = $track.track_file_style_conditional.track_input_bed_single line_width = $track.track_file_style_conditional.line_width type = vlines #end if ## Hlines: #if $track.track_file_style_conditional.track_file_style_selector == "hlines_track_option": [hlines_$counter] #if $track.track_file_style_conditional.title: title = $track.track_file_style_conditional.title #end if #if $track.track_file_style_conditional.height: height = $track.track_file_style_conditional.height #end if #if $track.track_file_style_conditional.min_value != "": min_value = $track.track_file_style_conditional.min_value #end if #if $track.track_file_style_conditional.max_value != "": max_value = $track.track_file_style_conditional.max_value #end if y_values = $track.track_file_style_conditional.y_values show_data_range = $track.track_file_style_conditional.show_data color = $track.track_file_style_conditional.color alpha = $track.track_file_style_conditional.alpha line_width = $track.track_file_style_conditional.line_width line_style = $track.track_file_style_conditional.line_style #if $track.track_file_style_conditional.invert_orientation: orientation = inverted #end if overlay_previous = $track.track_file_style_conditional.overlay_select file_type = hlines ## If spacer is asked a new section is created: #if $track.track_file_style_conditional.spacer_height != "": [spacer] height = $track.track_file_style_conditional.spacer_height #end if #end if ## Spacer #if $track.track_file_style_conditional.track_file_style_selector == "spacer_option": [spacer] #if $track.track_file_style_conditional.title: title = $track.track_file_style_conditional.title #end if #if $track.track_file_style_conditional.spacer_height != "": height = $track.track_file_style_conditional.spacer_height #end if #end if ## Xaxis: #if $track.track_file_style_conditional.track_file_style_selector == "xaxis_option": [x-axis] #if $track.track_file_style_conditional.title: title = $track.track_file_style_conditional.title #end if #if $track.track_file_style_conditional.fontsize != "": fontsize = $track.track_file_style_conditional.fontsize #end if where = $track.track_file_style_conditional.xaxis_where ## If spacer is asked a new section is created: #if $track.track_file_style_conditional.spacer_height != "": [spacer] height = $track.track_file_style_conditional.spacer_height #end if #end if ## Scale bar: #if $track.track_file_style_conditional.track_file_style_selector == "scale_bar_option": [scale_bar] #if $track.track_file_style_conditional.title: title = $track.track_file_style_conditional.title #end if #if $track.track_file_style_conditional.color != "": color = $track.track_file_style_conditional.color #end if alpha = $track.track_file_style_conditional.alpha line_width = $track.track_file_style_conditional.line_width #if $track.track_file_style_conditional.scalebar_pos.x_center != "": x_center = $track.track_file_style_conditional.scalebar_pos.x_center #end if #if $track.track_file_style_conditional.scalebar_pos.size != "": size = $track.track_file_style_conditional.scalebar_pos.size #end if #if $track.track_file_style_conditional.scalebar_pos.scalebar_start_position != "": scalebar_start_position = $track.track_file_style_conditional.scalebar_pos.scalebar_start_position #end if #if $track.track_file_style_conditional.scalebar_pos.scalebar_end_position != "": scalebar_end_position = $track.track_file_style_conditional.scalebar_pos.scalebar_end_position #end if where = $track.track_file_style_conditional.sb_where #if $track.track_file_style_conditional.fontsize != "": fontsize = $track.track_file_style_conditional.fontsize #end if file_type = scalebar ## If spacer is asked a new section is created: #if $track.track_file_style_conditional.spacer_height != "": [spacer] height = $track.track_file_style_conditional.spacer_height #end if #end if #end for </configfile> </configfiles> <inputs> <!--Arguments for pgt--> <param argument="--region" type="text" label="Region of the genome to limit the operation" optional="false" help="The format is chr:start-end, for example chr10:10-500"> <validator type="expression" message="Region should be like chr10:10-500">'^[a-zA-Z0-9_]:\d+-\d+$'</validator> </param> <section name="global_args" title="Configure figure parameters" expanded="False"> <param argument="--title" type="text" label="Plot title" help="If set, you may need to start by a spacer track"/> <param argument="--fontsize" type="integer" label="Font size for the labels of the plot" value="12"/> <param argument="--dpi" type="integer" label="Resolution (dpi)" value="72" help="Resolution for the image in case the ouput is a raster graphics image (e.g png, jpg)"/> <param argument="--width" type="float" label="Figure width in cm" value="40"/> <param argument="--plotWidth" type="float" label="Width in centimeters of the plotting (central) part" optional="true" help="This will overwrite what has been defined as a figure width."/> <param argument="--height" type="float" label="Figure height in centimeters" optional="true" help="If not given, the figure height is computed based on the heights of the tracks. If given, the track height are proportionally scaled to match the desired figure height."/> <param argument="--trackLabelFraction" type="float" label="Proportion of space dedicated to track labels" value="0.05" min="0" max="1"/> <param argument="--trackLabelHAlign" type="select" label="Horizontal alignment of track labels"> <option value="left" selected="True">left</option> <option value="right">right</option> <option value="center">center</option> </param> <param argument="--decreasingXAxis" type="boolean" truevalue="--decreasingXAxis" falsevalue="" checked="false" label="Use a decreasing x axis" help="By default, the x-axis is increasing. Use this option if you want to see all tracks with a decreasing x-axis."/> </section> <!--Info to build the config file--> <repeat name="tracks" min="1" title="Include tracks in your plot" help="Tracks can be of different filetypes. E.g BED, HiC-Matrix, BigWig or BedGraph. The order you add them represent the order they will be plotted from top to bottom."> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" type="select" label="Choose style of the track"> <option value="hic_matrix_option">TAD visualization</option> <option value="chrom_states_option">Chromatine states</option> <option value="gene_track_option">Gene track / Bed track</option> <option value="link_track_option">Link track</option> <option value="narrow_peak_track_option">NarrowPeak track</option> <option value="bigwig_track_option">Bigwig track</option> <option value="bedgraph_track_option">Bedgraph track </option> <option value="bedgraph_matrix_track_option">Bedgraph matrix track/TAD score</option> <option value="vlines_track_option">Vlines track</option> <option value="hlines_track_option">Hlines track</option> <option value="spacer_option">Spacer</option> <option value="xaxis_option">X-axis</option> <option value="scale_bar_option">Scale bar track</option> </param> <when value="hic_matrix_option"> <expand macro="plot_title" /> <expand macro="matrix_h5_cooler_multiple_macro" /> <param name="colormap" type="select" label="Color map to use for the heatmap" help="Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html"> <option value="RdYlBu_r">RdYlBu reversed</option> <option value="viridis">viridis</option> <expand macro="colormap_macro_noRdYlBu_r_noViridis"/> </param> <param name="depth" type="integer" value="8000000" optional="True" label="Depth" /> <expand macro="minmax_macro" /> <param name="transform" type="select" label="Plot the transformed value"> <option value="log1p" selected="True" >log1p</option> <option value="log">log</option> <option value="-log">-log</option> <option value="no">no transformation</option> </param> <param name="height_matrix" type="float" value="" optional="True" label="height"/> <param name="show_masked_bins" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show masked bins" /> <param name="boundaries_file" type="data" optional="True" format="bed" label="Boundaries file" multiple="True"/> <param name="scale_factor" type="float" value="1.0" optional="True" label="Scale factor" help="if the values in the matrix need to be scaled the following parameter can be used" /> <param name="rasterize" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Rasterize the heatmap" /> <expand macro="inverted_macro" /> <expand macro="spacer_macro" /> </when> <when value="chrom_states_option"> <expand macro="plot_title" /> <expand macro="track_input_bed_macro" /> <conditional name="color_bed"> <param name="color_bed_select" type="select" label="Define color:"> <option value="manually" selected="True">manually</option> <option value="bed_rgb">From the 9th field</option> <option value="colormap">From the 5th field (score)</option> </param> <when value="manually"> <param name="color" type="color" value="#000000" label="Color of track" optional="True" /> </when> <when value="bed_rgb" /> <when value="colormap"> <param name="color" type="select" label="Color map to use for the scores" help=" Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html"> <option value="RdYlBu_r">RdYlBu reversed</option> <option value="viridis">viridis</option> <expand macro="colormap_macro_noRdYlBu_r_noViridis" /> </param> </when> </conditional> <expand macro="border_color_bed_macro" /> <param name="line_width" type="float" value="0.5" label="width of lines" /> <param name="height_chrom" type="float" value="1.5" optional="True" label="height"/> <param name="labels" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Plot labels" /> <expand macro="spacer_macro" /> </when> <when value="gene_track_option"> <expand macro="plot_title" /> <expand macro="track_input_bed_gtf_macro" /> <conditional name="color_bed"> <param name="color_bed_select" type="select" label="Define color:"> <option value="manually" selected="True">manually</option> <option value="bed_rgb">From the 9th field</option> <option value="colormap">From the 5th field (score)</option> </param> <when value="manually"> <param name="color" type="color" value="#000000" label="Color of track" optional="True" /> </when> <when value="bed_rgb" /> <when value="colormap"> <param name="color" type="select" label="Color map to use for the scores" help=" Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html"> <option value="RdYlBu_r">RdYlBu reversed</option> <option value="viridis">viridis</option> <expand macro="colormap_macro_noRdYlBu_r_noViridis" /> </param> </when> </conditional> <expand macro="border_color_bed_macro" /> <param name="height_bed" type="float" value="1.5" optional="True" label="height"/> <conditional name="labels"> <param name="plot_labels" type="select" label="Plot labels"> <option value="true" selected="True">yes</option> <option value="false">no</option> </param> <when value="true"> <param name="all_labels_inside" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Put all labels inside the plotted region" help="Put labels on the left of the region if the region ends after the plotted region."/> <param name="labels_in_margin" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Allow to put labels in the right margin" help="Put labels in the margin if the region ends after the plotted region."/> </when> <when value="false"/> </conditional> <param name="display" type="select" label="display to use"> <option value="stacked" selected="True">stacked (no overlap even with the label)</option> <option value="interleaved">interleaved (everything on 2 lines)</option> <option value="collapsed">collapsed (everything on 1 line)</option> <option value="triangles">triangles (plot triangles between start and end)</option> </param> <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" /> <conditional name="bed_style"> <param name="bed_style_select" type="select" label="Bed style"> <option value="flybase" selected="True">flybase (blocks with arrow at extremities)</option> <option value="UCSC">UCSC (blocks with arrows in introns)</option> <option value="tssarrow">tssarrow (blocks with arrow above at beginning)</option> </param> <when value="flybase"> <param name="arrowhead_included" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Include the arrowhead in the bed interval:" help="When set to False, the arrow indicating the orientation of the interval is plotted outside of the interval."/> <section name="bed_advanced" title="Configure other bed parameters" expanded="False"> <expand macro="utr_macro" /> <expand macro="bed_advanced_macro" /> </section> </when> <when value="UCSC"> <section name="bed_advanced" title="Configure other bed parameters" expanded="False"> <param name="arrow_interval" type="integer" value="2" min="0" label="interval between 2 arrows on introns in UCSC style"/> <expand macro="bed_advanced_macro" /> </section> </when> <when value="tssarrow"> <section name="bed_advanced" title="Configure other bed parameters" expanded="False"> <param name="arrow_length" type="integer" optional="true" label="arrow length" help="the length of the arrow in bp (default is 4% of the plotted region)"/> <expand macro="utr_macro" /> <expand macro="bed_advanced_macro" /> </section> </when> </conditional> <expand macro="overlay_macro" /> <expand macro="inverted_macro" /> <expand macro="spacer_macro" /> </when> <when value="link_track_option"> <expand macro="plot_title" /> <expand macro="track_input_link_macro" /> <conditional name="color_link"> <param name="color_link_select" type="select" label="Define color:"> <option value="manually" selected="True">manually</option> <option value="colormap">From the 7th field (score)</option> </param> <when value="manually"> <param name="color" type="color" value="#000000" label="Color of track" optional="True" /> </when> <when value="colormap"> <param name="color" type="select" label="Color map to use for the scores" help=" Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html"> <option value="RdYlBu_r">RdYlBu reversed</option> <option value="viridis">viridis</option> <expand macro="colormap_macro_noRdYlBu_r_noViridis" /> </param> </when> </conditional> <expand macro="lines_macro" /> <param name="links_type" type="select" label="Representation of the link:"> <option value="arcs" selected="True">arcs (a line between the centers of the 2 regions)</option> <option value="triangles">triangles</option> <option value="loops">loops (a rectangle highlighting the intersection)</option> </param> <param name="compact_arcs_level" type="select" label="Height of arcs and triangles:"> <option value="0" selected="True">default (proportional to distance)</option> <option value="1">compacted (the height is proportional to the square root of the distance)</option> <option value="2">highly compacted (the height is the same for all distances)</option> </param> <param name="ylim" type="float" optional="True" label="ylim" help="To be able to see small arcs when big arcs exists, you can set the upper y limit. The unit is bp. This corresponds to the longest arc you will see not truncated."/> <param name="use_middle" type="select" label="Coordinates to use" help="Not useful with loops"> <option value="false" selected="True">Extremities (start of first and end of second)</option> <option value="true">Center (mean of start and end for each)</option> </param> <param name="height" type="float" value="1.5" optional="True" label="height"/> <expand macro="minmax_macro" /> <expand macro="overlay_macro" /> <expand macro="inverted_macro" /> <expand macro="spacer_macro" /> </when> <when value="narrow_peak_track_option"> <expand macro="plot_title" /> <expand macro="track_input_narrow_peak_macro" /> <param name="color" type="color" value="#000000" label="Color of track" optional="True" /> <param name="height_narrow_peak" type="float" value="1.5" optional="True" label="height"/> <conditional name="display"> <param name="display_selector" type="select" label="display to use"> <option value="peak" selected="True">peak: Draw a peak shape from start, end, summit, height</option> <option value="box">box: Draw a box</option> </param> <when value="peak"> <param name="use_summit" type="boolean" truevalue="true" falsevalue="false" checked="true" optional="True" label="Use summit information to make the curve." /> <param name="show_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show visualization of data range" /> <param name="width_adjust" type="float" value="1.5" optional="True" label="Factor to change the width of the curve."/> <expand macro="minmax_macro" /> </when> <when value="box"> <param name="use_summit" type="boolean" truevalue="true" falsevalue="false" checked="true" optional="True" label="Plot a vertical bar at the summit position." /> </when> </conditional> <param name="line_width" type="float" value="1" label="width of lines" /> <param name="show_labels" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Plot labels (name, p-val, q-val)" /> <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" /> <expand macro="overlay_macro" /> <expand macro="inverted_macro" /> <expand macro="spacer_macro" /> </when> <when value="bedgraph_track_option"> <expand macro="plot_title" /> <expand macro="track_input_bedgraph_macro" /> <expand macro="color_coverage_macro" /> <expand macro="minmax_macro" /> <param name="height_bedgraph" type="float" value="1.5" optional="True" label="height"/> <expand macro="type_coverage_macro" /> <section name="reading_bdg_as_bw" title="Configure bigwig parameters" expanded="False"> <param name="summary_method" type="select" label="Summary method"> <option value="no" selected="True">no=no summary method (keep all values)</option> <option value="mean">mean=mean value</option> <option value="min">min=minimum value</option> <option value="max">max=maximum value</option> <option value="coverage">coverage=number of covered bases</option> <option value="std">std=standard deviation</option> </param> <param name="number_of_bins" type="integer" value="" optional="True" label="Number of bins" /> </section> <expand macro="logScale_coverage_macro" /> <section name ="op" title="Compute an operation on the file" expanded="False"> <param name="operation" type="text" label="operation to compute on the file(s)" value="file" help="operation will be evaluated, it should contains file or file and second_file, for example `0.89 * file` `- file` `file - second_file` `log2((1 + file) / (1 + second_file))` or `max(file, second_file)`"/> <param name="second_file" type="data" format="bedgraph" label="second_file (bedgraph format)" multiple="False" optional="True"/> </section> <param name="nans_to_zeros" type="boolean" truevalue="true" falsevalue="false" checked="false" label="NAN's to zeros" /> <param name="use_middle" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use middle: Instead of using start and end, use the middle of intervals (useful for 4C-seq tracks)." /> <param name="show_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show visualization of data range" /> <param name="grid" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Display a grid on the y-axis" /> <expand macro="inverted_macro" /> <expand macro="overlay_macro" /> <expand macro="spacer_macro" /> </when> <when value="bigwig_track_option"> <expand macro="plot_title" /> <expand macro="track_input_bigwig_macro" /> <expand macro="color_coverage_macro" /> <expand macro="minmax_macro" /> <param name="height_bigwig" type="float" value="1.5" optional="True" label="height"/> <section name="reading_bw_conditional" title="Configure bigwig parameters" expanded="False"> <param name="summary_method" type="select" label="Summary method"> <option value="mean" selected="True">mean=mean value</option> <option value="min">min=minimum value</option> <option value="max">max=maximum value</option> <option value="coverage">coverage=number of covered bases</option> <option value="std">std=standard deviation</option> </param> <param name="number_of_bins" type="integer" value="" optional="True" label="Number of bins" /> <param name="nans_to_zeros" type="boolean" truevalue="true" falsevalue="false" checked="false" label="NAN's to zeros" /> </section> <expand macro="type_coverage_macro" /> <expand macro="logScale_coverage_macro" /> <section name ="op" title="Compute an operation on the file" expanded="False"> <param name="operation" type="text" label="operation to compute on the file(s)" value="file" help="operation will be evaluated, it should contains file or file and second_file, for example `0.89 * file` `- file` `file - second_file` `log2((1 + file) / (1 + second_file))` or `max(file, second_file)`"/> <param name="second_file" type="data" format="bigwig" label="second_file (bedgraph format)" multiple="False" optional="True"/> </section> <param name="show_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show visualization of data range"/> <param name="grid" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Display a grid on the y-axis" /> <expand macro="inverted_macro" /> <expand macro="overlay_macro" /> <expand macro="spacer_macro" /> </when> <when value="bedgraph_matrix_track_option"> <expand macro="plot_title" /> <expand macro="track_input_bedgraph_matrix_macro" /> <expand macro="minmax_macro" /> <param name="height_bedgraph" type="float" value="1.5" optional="True" label="height"/> <conditional name="type"> <param name="type_selector" type="select" label="type of plotting"> <option value="lines" selected="True">lines: each column in the bedgraph will be a line and a mean line will be added</option> <option value="matrix">matrix: each column in the bedgraph will be a raw in the matrix</option> </param> <when value="lines"> <param name="plot_horizontal_lines" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Plot an horizontal line at 0 when type is lines" /> <param name="show_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show visualization of data range" /> <param name="pos_score_in_bin" type="select" label="Position of the score with respect to bin start and end"> <option value="center" selected="True">Center</option> <option value="block">Block (draw a horizontal line between start and end)</option> </param> </when> <when value="matrix"> <param name="colormap" type="select" label="colormap"> <option value="viridis">viridis</option> <option value="RdYlBu_r">RdYlBu reversed</option> <expand macro="colormap_macro_noRdYlBu_r_noViridis" /> </param> </when> </conditional> <expand macro="inverted_macro" /> <expand macro="spacer_macro" /> </when> <when value="vlines_track_option"> <expand macro="track_input_bed_single_macro" /> <param name="line_width" type="float" value="0.5" label="width of lines"/> </when> <when value="hlines_track_option"> <expand macro="plot_title" /> <param name="y_values" type="text" value="10, 200" label="Values where horizontal lines should be plotted separated by comma"/> <param name="color" type="color" value="#000000" label="Color of line(s)" optional="True" /> <expand macro="lines_macro" /> <param name="height" type="float" value="1.5" optional="True" label="height"/> <expand macro="minmax_macro" /> <param name="show_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show visualization of data range"/> <expand macro="inverted_macro" /> <expand macro="overlay_macro" /> <expand macro="spacer_macro" /> </when> <when value="spacer_option"> <expand macro="plot_title" /> <param name="spacer_height" type="float" value="" optional="True" label="Height of the spacer."/> </when> <when value="xaxis_option"> <expand macro="plot_title" /> <param name="fontsize" type="float" optional="True" label="Fontsize of the x-axis."/> <param name="xaxis_where" type="select" label="chromosome name and coordinates position relative to the axis"> <option value="bottom" selected="True">below</option> <option value="top">above</option> </param> <expand macro="spacer_macro" /> </when> <when value="scale_bar_option"> <expand macro="plot_title" /> <param name="color" type="color" label="Color of the scale bar" optional="True" /> <param name="alpha" type="float" value="1" min="0" max="1" label="level of transparency (alpha)" help="1 is opaque and 0 is totally transparent"/> <param name="line_width" type="float" value="0.5" label="width of lines"/> <section name="scalebar_pos" title="Set the scalebar position" expanded="true" help="You can optionally define one or multiple parameters below."> <param name="scalebar_start_position" type="integer" label="coordinate where the scale bar should begin." optional="True"/> <param name="scalebar_end_position" type="integer" label="coordinate where the scale bar should end." optional="True"/> <param name="x_center" type="integer" label="coordinate where the scale bar should be plotted (center)" optional="True" help="If not set and cannot be deduced from others it will be in the middle of the plotted area."/> <param name="size" type="integer" label="size of the scale bar" optional="True" help="If not set and cannot be deduced from others it will be the higher number that begins with 1, 2 or 5 followed by 0s that is less than half the plotted area."/> </section> <param name="sb_where" type="select" label="where the size of the scale bar should appear relative to the bar"> <option value="left" selected="True">left</option> <option value="right">right</option> <option value="bottom">below</option> <option value="top">above</option> </param> <param name="fontsize" type="float" optional="True" label="Fontsize of the size of the scale bar."/> <expand macro="spacer_macro" /> </when> </conditional> </repeat> <param name="image_file_format" type="select" label="Image output format"> <option value="png">png</option> <option value="svg">svg</option> </param> </inputs> <outputs> <data format="png" name="outFileName" from_work_dir="plot" label="${tool.name} on [${on_string}]: Plot"> <change_format> <when input="image_file_format" value="png" format="png" /> <when input="image_file_format" value="svg" format="svg" /> </change_format> </data> </outputs> <tests> <!--test 1--> <test> <param name="region" value="chrX:3000000-3500000"/> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="xaxis_option" /> <param name="xaxis_where" value="top" /> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="hic_matrix_option" /> <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/> <param name="title" value="Kc DpnII (Li et al. 2015)" /> <!--<param name="colormap" value="RdYlBu_r" />--> <param name="depth" value="200000" /> <param name="transform" value="log1p" /> <param name="boundaries_file" value="domains.bed" /> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="spacer_option" /> <param name="spacer_height" value="0.05" /> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="chrom_states_option" /> <param name="track_input_bed" value="tad_classification.bed" ftype="bed" /> <param name="title" value="TAD state" /> <param name="height_chrom" value="0.5" /> <param name="labels" value="false" /> <conditional name="color_bed"> <param name="color_bed_select" value="bed_rgb" /> </conditional> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="bedgraph_matrix_track_option" /> <param name="track_input_bedgraph_matrix" value="tad_score.gz" ftype="bedgraph" /> <param name="title" value="TAD separation score (Ramirez et al.)" /> <conditional name="type"> <param name="type_selector" value="matrix" /> <!--<param name="colormap" value="viridis" />--> </conditional> <param name="height_bedgraph" value="10" /> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="spacer_option" /> <param name="spacer_height" value="1" /> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="bedgraph_track_option" /> <param name="track_input_bedgraph" value="bedgraph_chrx_2e6_5e6.bg" ftype="bedgraph" /> <param name="title" value="bedgraph" /> <param name="height_bedgraph" value="4" /> <param name="color" value="blue" /> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="bigwig_track_option" /> <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" /> <param name="title" value="rep 1 test fill" /> <param name="height_bigwig" value="4" /> <param name="color" value="blue" /> <conditional name="type_conditional"> <param name="type_selector" value="fill_option" /> </conditional> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="bigwig_track_option" /> <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" /> <param name="title" value="rep 1 test line" /> <param name="height_bigwig" value="4" /> <param name="color" value="red" /> <conditional name="type_conditional"> <param name="type_selector" value="line_option" /> <param name="width_line" value="1" /> </conditional> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="bigwig_track_option" /> <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" /> <param name="title" value="rep 1 test lw=0.2" /> <param name="height_bigwig" value="4" /> <param name="color" value="red" /> <conditional name="type_conditional"> <param name="type_selector" value="line_option" /> <param name="width_line" value="0.1" /> </conditional> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="bigwig_track_option" /> <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" /> <param name="title" value="rep 1 test point:0.5" /> <param name="height_bigwig" value="4" /> <param name="color" value="black" /> <conditional name="type_conditional"> <param name="type_selector" value="point_option" /> <param name="width_point" value="0.5" /> </conditional> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="spacer_option" /> <param name="spacer_height" value="0.5" /> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="gene_track_option" /> <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" /> <param name="title" value="genes" /> <param name="height_bed" value="5" /> <param name="fontsize" value="10" /> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="spacer_option" /> <param name="spacer_height" value="1" /> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="gene_track_option" /> <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" /> <param name="title" value="max num rows 3" /> <param name="height_bed" value="3" /> <param name="fontsize" value="8" /> <conditional name="bed_style"> <section name="bed_advanced"> <param name="gene_rows" value="3" /> </section> </conditional> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="spacer_option" /> <param name="spacer_height" value="1" /> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="gene_track_option" /> <param name="track_input_bed" value="dm3_genes.bed6.gz" ftype="bed" /> <param name="title" value="bed6 global max row" /> <param name="height_bed" value="20" /> <param name="fontsize" value="10" /> <conditional name="bed_style"> <section name="bed_advanced"> <param name="global_max_row" value="true" /> </section> </conditional> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="vlines_track_option" /> <param name="track_input_bed_single" value="domains.bed" ftype="bed" /> </conditional> </repeat> <param name="image_file_format" value="png" /> <output name="outFileName" file="master_TADs_plot.png" ftype="png" compare="sim_size" delta="100" /> </test> <!--test 2--> <test> <param name="region" value="chrX:3000000-3500000"/> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="xaxis_option" /> <param name="xaxis_where" value="top" /> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="bigwig_track_option" /> <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw,bigwig_chrx_2e6_5e6.bw" ftype="bigwig" /> <param name="title" value="rep 1 test line" /> <param name="height_bigwig" value="4" /> <param name="color" value="red" /> <conditional name="type_conditional"> <param name="type_selector" value="line_option" /> <param name="width_line" value="1" /> </conditional> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="bigwig_track_option" /> <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" /> <param name="title" value="nans_to_zeros" /> <param name="height_bigwig" value="4" /> <param name="color" value="blue" /> <section name="reading_bw_conditional"> <param name="nans_to_zeros" value="true" /> </section> <param name="show_data" value="true" /> <conditional name="type_conditional"> <param name="type_selector" value="line_option" /> <param name="width_line" value="1" /> </conditional> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="hlines_track_option" /> <param name="title" value="" /> <param name="color" value="orange" /> <param name="y_values" value="50" /> <param name="line_width" value="2" /> <param name="line_style" value="dashed" /> <param name="overlay_select" value="share-y" /> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="hlines_track_option" /> <param name="title" value="hlines" /> <param name="color" value="purple" /> <param name="y_values" value="0, 10, 20, 100" /> <param name="min_value" value="12" /> <param name="show_data" value="true" /> <param name="invert_orientation" value="true" /> </conditional> </repeat> <param name="image_file_format" value="png" /> <output name="outFileName" file="bigwig_multiple.png" ftype="png" compare="sim_size" delta="100" /> </test> <!--test 3--> <test> <param name="region" value="chrX:3000000-3500000"/> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="xaxis_option" /> <param name="xaxis_where" value="top" /> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="hic_matrix_option" /> <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/> <param name="title" value="Kc DpnII (Li et al. 2015) log1p" /> <param name="colormap" value="RdYlBu_r" /> <param name="depth" value="200000" /> <param name="transform" value="log1p" /> <param name="boundaries_file" value="domains.bed" /> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="chrom_states_option" /> <param name="track_input_bed" value="tad_classification.bed" ftype="bed" /> <param name="title" value="TAD state" /> <param name="height_chrom" value="0.5" /> <param name="labels" value="false" /> <conditional name="color_bed"> <param name="color_bed_select" value="bed_rgb" /> </conditional> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="hic_matrix_option" /> <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/> <param name="title" value="Kc DpnII (Li et al. 2015) inverted no transform" /> <param name="colormap" value="Reds" /> <param name="depth" value="200000" /> <param name="transform" value="no" /> <param name="invert_orientation" value="true" /> <param name="min_value" value="5" /> <param name="max_value" value="70" /> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="spacer_option" /> <param name="spacer_height" value="1" /> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="bedgraph_track_option" /> <param name="track_input_bedgraph" value="test_with_neg_values.bg.gz" ftype="bedgraph" /> <param name="title" value="bedgraph with negative values" /> <param name="height_bedgraph" value="4" /> <param name="color" value="black" /> <conditional name="color_negative"> <param name="color_negative_select" value="true" /> <param name="color" value="red" /> </conditional> <conditional name="type_conditional"> <param name="type_selector" value="fill_option" /> </conditional> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="bedgraph_track_option" /> <param name="track_input_bedgraph" value="bedgraph_chrx_2e6_5e6.bg" ftype="bedgraph" /> <param name="title" value="bedgraph" /> <param name="height_bedgraph" value="4" /> <param name="color" value="blue" /> <conditional name="type_conditional"> <param name="type_selector" value="fill_option" /> </conditional> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="bigwig_track_option" /> <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" /> <param name="title" value="rep 1 test fill" /> <param name="height_bigwig" value="4" /> <param name="color" value="blue" /> <conditional name="type_conditional"> <param name="type_selector" value="fill_option" /> </conditional> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="bigwig_track_option" /> <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" /> <param name="title" value="(red points/width=5/max value/100 bins) overlayed with (dark red line/min value/30000 bins) overlayed with (black line/min value)" /> <param name="height_bigwig" value="10" /> <param name="color" value="red" /> <conditional name="type_conditional"> <param name="type_selector" value="point_option" /> <param name="width_point" value="5" /> </conditional> <section name="reading_bw_conditional"> <param name="summary_method" value="max"/> <param name="number_of_bins" value="100"/> </section> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="bigwig_track_option" /> <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" /> <param name="height_bigwig" value="10" /> <param name="color" value="#c00000" /> <conditional name="type_conditional"> <param name="type_selector" value="line_option" /> </conditional> <section name="reading_bw_conditional"> <param name="summary_method" value="min"/> </section> <param name="overlay_select" value="share-y" /> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="bigwig_track_option" /> <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" /> <param name="height_bigwig" value="10" /> <param name="color" value="black" /> <conditional name="type_conditional"> <param name="type_selector" value="line_option" /> </conditional> <section name="reading_bw_conditional"> <param name="summary_method" value="min"/> <param name="number_of_bins" value="30000"/> </section> <param name="overlay_select" value="share-y" /> <param name="spacer_height" value="1" /> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="gene_track_option" /> <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" /> <param name="title" value="genes in ucsc" /> <param name="height_bed" value="5" /> <param name="fontsize" value="10" /> <conditional name="bed_style"> <param name="bed_style_select" value="UCSC"/> </conditional> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="gene_track_option" /> <param name="track_input_bed" value="dm3_genes.bed6.gz" ftype="bed" /> <param name="title" value="bed6 global max row color from score" /> <param name="height_bed" value="20" /> <param name="fontsize" value="10" /> <conditional name="bed_style"> <section name="bed_advanced"> <param name="global_max_row" value="true" /> </section> </conditional> <conditional name="color_bed"> <param name="color_bed_select" value="colormap" /> <param name="color" value="RdYlBu_r" /> </conditional> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="gene_track_option" /> <param name="track_input_bed" value="domains.bed" ftype="bed" /> <param name="title" value="domains.bed using the 9th field for colors interleaved border=red" /> <param name="height_bed" value="2" /> <param name="fontsize" value="10" /> <conditional name="color_bed"> <param name="color_bed_select" value="bed_rgb" /> </conditional> <conditional name="border_color_bed"> <param name="border_color_bed_select" value="manually" /> <param name="color" value="red" /> </conditional> <conditional name="labels"> <param name="plot_labels" value="false" /> </conditional> <param name="display" value="interleaved" /> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="gene_track_option" /> <param name="track_input_bed" value="domains.bed" ftype="bed" /> <param name="title" value="domains.bed using the 9th field for colors interleaved border=bed_rgb" /> <param name="height_bed" value="2" /> <param name="fontsize" value="10" /> <conditional name="color_bed"> <param name="color_bed_select" value="bed_rgb" /> </conditional> <conditional name="border_color_bed"> <param name="border_color_bed_select" value="bed_rgb" /> </conditional> <conditional name="labels"> <param name="plot_labels" value="false" /> </conditional> <param name="display" value="interleaved" /> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="gene_track_option" /> <param name="track_input_bed" value="domains.bed" ftype="bed" /> <param name="title" value="domains.bed using the 9th field for colors interleaved border=none" /> <param name="height_bed" value="2" /> <param name="fontsize" value="10" /> <conditional name="color_bed"> <param name="color_bed_select" value="bed_rgb" /> </conditional> <conditional name="border_color_bed"> <param name="border_color_bed_select" value="none" /> </conditional> <conditional name="labels"> <param name="plot_labels" value="false" /> </conditional> <param name="display" value="interleaved" /> </conditional> </repeat> <param name="image_file_format" value="png" /> <output name="outFileName" file="master_TADs_BW_plot.png" ftype="png" compare="sim_size" delta="100" /> </test> <!--test 4--> <test> <param name="region" value="X:2700000-3100000"/> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="bigwig_track_option" /> <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" /> <param name="title" value="(bigwig color=blue 2000 bins) overlayed with (bigwig mean color=red alpha = 0.5 max over 300 bins)" /> <param name="height_bigwig" value="7" /> <param name="color" value="#00b0f0" /> <section name="reading_bw_conditional"> <param name="number_of_bins" value="2000"/> </section> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="bigwig_track_option" /> <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" /> <param name="title" value="" /> <param name="color" value="#ff0000" /> <param name="alpha" value="0.5" /> <param name="summary_method" value="max" /> <section name="reading_bw_conditional"> <param name="number_of_bins" value="300"/> </section> <param name="overlay_select" value="share-y"/> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="xaxis_option" /> <param name="xaxis_where" value="bottom" /> </conditional> </repeat> <param name="image_file_format" value="png" /> <output name="outFileName" file="test_alpha.png" ftype="png" compare="sim_size" delta="100" /> </test> <!--test 5--> <test> <param name="region" value="X:3000000-3300000"/> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="xaxis_option" /> <param name="xaxis_where" value="top" /> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="gene_track_option" /> <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" /> <param name="title" value="test" /> <param name="height_bed" value="10" /> <param name="color" value="#000000" /> <conditional name="bed_style"> <param name="bed_style_select" value="UCSC"/> </conditional> <param name="spacer_height" value="1"/> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="gene_track_option" /> <param name="track_input_bed" value="dm3_subset_BDGP5.78_asbed4.bed.gz" ftype="bed" /> <param name="title" value="test" /> <param name="height_bed" value="10" /> <param name="color" value="#000000" /> <conditional name="bed_style"> <param name="bed_style_select" value="UCSC"/> </conditional> <param name="spacer_height" value="1"/> </conditional> </repeat> <param name="image_file_format" value="png" /> <output name="outFileName" file="test_gtf_bed4.png" ftype="png" compare="sim_size" delta="100" /> </test> <!--test 6--> <test> <param name="region" value="X:2760000-2802000"/> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="narrow_peak_track_option" /> <param name="title" value="box" /> <param name="track_input_narrow_peak" value="test2.narrowPeak" ftype="encodepeak" /> <param name="color" value="#9bbb59" /> <param name="height_narrow_peak" value="4" /> <conditional name="display"> <param name="display_selector" value="box" /> <param name="use_summit" value="true" /> </conditional> <param name="show_labels" value="true" /> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="narrow_peak_track_option" /> <param name="title" value="box line_width = 2" /> <param name="track_input_narrow_peak" value="test2.narrowPeak" ftype="encodepeak" /> <param name="color" value="#9bbb59" /> <param name="height_narrow_peak" value="4" /> <param name="line_width" value="2" /> <conditional name="display"> <param name="display_selector" value="box" /> <param name="use_summit" value="true" /> </conditional> <param name="show_labels" value="true" /> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="narrow_peak_track_option" /> <param name="title" value="peak width 3" /> <param name="track_input_narrow_peak" value="test2.narrowPeak" ftype="encodepeak" /> <param name="color" value="#c0504d" /> <param name="height_narrow_peak" value="4" /> <conditional name="display"> <param name="display_selector" value="peak" /> <param name="use_summit" value="true" /> <param name="show_data" value="true" /> <param name="width_adjust" value="3" /> <param name="max_value" value="50" /> </conditional> <param name="show_labels" value="false" /> <param name="spacer_height" value="0.5"/> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="narrow_peak_track_option" /> <param name="title" value="peak no data range" /> <param name="track_input_narrow_peak" value="test2.narrowPeak" ftype="encodepeak" /> <param name="color" value="#000000" /> <param name="height_narrow_peak" value="4" /> <conditional name="display"> <param name="display_selector" value="peak" /> <param name="use_summit" value="false" /> <param name="show_data" value="false" /> </conditional> <param name="show_labels" value="true" /> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="xaxis_option" /> <param name="xaxis_where" value="bottom" /> </conditional> </repeat> <param name="image_file_format" value="png" /> <output name="outFileName" file="test_narrowPeak.png" ftype="png" compare="sim_size" delta="100" /> </test> <!--test 7--> <test> <param name="region" value="chrX:3300000-3500000"/> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="xaxis_option" /> <param name="xaxis_where" value="top" /> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="gene_track_option" /> <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" /> <param name="title" value="genes" /> <param name="height_bed" value="10" /> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="gene_track_option" /> <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" /> <param name="title" value="gtf" /> <param name="height_bed" value="10" /> <conditional name="bed_style"> <section name="bed_advanced"> <param name="height_utr" value="0.75"/> <conditional name="color_utr"> <param name="color_utr_select" value="manually"/> <param name="color" value="#ff0000"/> </conditional> <section name ="gtf"> <param name="prefered_name" value="gene_name"/> <param name="merge_transcripts" value="true"/> </section> </section> </conditional> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="gene_track_option" /> <param name="track_input_bed" value="dm3_genes_withrgbandscore.bed.gz" ftype="bed" /> <param name="title" value="genes with scores" /> <param name="height_bed" value="10" /> <conditional name="color_bed"> <param name="color_bed_select" value="colormap" /> <param name="color" value="cool_r" /> </conditional> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="gene_track_option" /> <param name="track_input_bed" value="dm3_genes_withrgbandscore.bed.gz" ftype="bed" /> <param name="title" value="genes with utr as bed_rgb" /> <param name="height_bed" value="10" /> <conditional name="bed_style"> <section name="bed_advanced"> <conditional name="color_utr"> <param name="color_utr_select" value="bed_rgb"/> </conditional> </section> </conditional> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="gene_track_option" /> <param name="track_input_bed" value="dm3_genes_withrgbandscore.bed.gz" ftype="bed" /> <param name="title" value="genes with coding as bed_rgb - labels_in_margin" /> <param name="height_bed" value="10" /> <conditional name="color_bed"> <param name="color_bed_select" value="bed_rgb" /> </conditional> <conditional name="labels"> <param name="plot_labels" value="true" /> <param name="labels_in_margin" value="true" /> </conditional> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="gene_track_option" /> <param name="track_input_bed" value="dm3_genes_withrgbandscore.bed.gz" ftype="bed" /> <param name="title" value="genes bed_rgb like - all_labels_inside" /> <param name="height_bed" value="10" /> <conditional name="color_bed"> <param name="color_bed_select" value="bed_rgb" /> </conditional> <conditional name="bed_style"> <section name="bed_advanced"> <conditional name="color_utr"> <param name="color_utr_select" value="like"/> </conditional> </section> </conditional> <conditional name="labels"> <param name="plot_labels" value="true" /> <param name="all_labels_inside" value="true" /> </conditional> </conditional> </repeat> <param name="image_file_format" value="png" /> <output name="outFileName" file="test_gtf_flybase_param.png" ftype="png" compare="sim_size" delta="100" /> </test> <!--test 8--> <test> <param name="region" value="chrX:3300000-3500000"/> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="xaxis_option" /> <param name="xaxis_where" value="top" /> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="gene_track_option" /> <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" /> <param name="title" value="dm3_genes.bed" /> <param name="height_bed" value="10" /> <conditional name="bed_style"> <param name="bed_style_select" value="UCSC"/> <section name="bed_advanced"> <param name="global_max_row" value="true" /> <param name="max_labels" value="15" /> </section> </conditional> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="gene_track_option" /> <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" /> <param name="title" value="genes.bed.gz" /> <param name="height_bed" value="10" /> <conditional name="bed_style"> <param name="bed_style_select" value="UCSC"/> <section name="bed_advanced"> <param name="arrow_interval" value="10"/> <param name="line_width" value="2"/> </section> </conditional> </conditional> </repeat> <param name="image_file_format" value="png" /> <output name="outFileName" file="test_ucsc_param.png" ftype="png" compare="sim_size" delta="100" /> </test> <!--test 9--> <test> <param name="region" value="X:3133000-3138000"/> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="xaxis_option" /> <param name="xaxis_where" value="top" /> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="gene_track_option" /> <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" /> <param name="title" value="test" /> <param name="height_bed" value="10" /> <param name="spacer_height" value="1"/> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="gene_track_option" /> <param name="track_input_bed" value="dm3_subset_BDGP5.78_asbed4.bed.gz" ftype="bed" /> <param name="title" value="test" /> <param name="height_bed" value="10" /> <conditional name="color_bed"> <param name="color_bed_select" value="manually" /> <param name="color" value="red" /> </conditional> <conditional name="bed_style"> <param name="bed_style_select" value="UCSC"/> </conditional> <param name="spacer_height" value="1"/> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="gene_track_option" /> <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" /> <param name="title" value="test" /> <param name="height_bed" value="10" /> <conditional name="color_bed"> <param name="color_bed_select" value="manually" /> <param name="color" value="red" /> </conditional> <param name="spacer_height" value="1"/> <conditional name="bed_style"> <param name="arrowhead_included" value="true"/> </conditional> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="vlines_track_option" /> <param name="track_input_bed_single" value="dm3_subset_BDGP5.78_asbed4.bed.gz" ftype="bed" /> </conditional> </repeat> <param name="image_file_format" value="png" /> <output name="outFileName" file="test_arrowhead_zoom.png" ftype="png" compare="sim_size" delta="100" /> </test> <!--test 10--> <test> <param name="region" value="X:3340000-3380000"/> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="xaxis_option" /> <param name="xaxis_where" value="top" /> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="gene_track_option" /> <param name="track_input_bed" value="domains.bed" ftype="bed" /> <param name="height_bed" value="6" /> <conditional name="color_bed"> <param name="color_bed_select" value="manually" /> <param name="color" value="yellow" /> </conditional> <param name="display" value="triangles" /> <param name="spacer_height" value="1"/> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="bedgraph_track_option" /> <param name="track_input_bedgraph" value="bedgraph_chrx_2e6_5e6.bg" ftype="bedgraph" /> <param name="title" value="bedgraph" /> <param name="height_bedgraph" value="4" /> <param name="color" value="blue" /> <conditional name="type_conditional"> <param name="type_selector" value="line_option" /> </conditional> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="bedgraph_track_option" /> <param name="track_input_bedgraph" value="bedgraph_chrx_2e6_5e6.bg" ftype="bedgraph" /> <param name="title" value="bedgraph" /> <param name="height_bedgraph" value="4" /> <param name="color" value="blue" /> <param name="use_middle" value="true" /> <conditional name="type_conditional"> <param name="type_selector" value="line_option" /> </conditional> </conditional> </repeat> <param name="image_file_format" value="png" /> <output name="outFileName" file="test_middle_triangle.png" ftype="png" compare="sim_size" delta="100" /> </test> <!--test 11--> <test> <param name="region" value="chrX:3250000-3400000"/> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="xaxis_option" /> <param name="xaxis_where" value="top" /> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="hic_matrix_option" /> <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/> <param name="title" value="Kc DpnII (Li et al. 2015)" /> <!--<param name="colormap" value="RdYlBu_r" />--> <param name="depth" value="100000" /> <param name="transform" value="log1p" /> <param name="show_masked_bins" value="true" /> <param name="scale_factor" value="2.0" /> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="spacer_option" /> <param name="spacer_height" value="0.05" /> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="bedgraph_matrix_track_option" /> <param name="track_input_bedgraph_matrix" value="tad_score.gz" ftype="bedgraph" /> <param name="title" value="TAD separation score (Ramirez et al.)" /> <param name="height_bedgraph" value="10" /> <conditional name="type"> <param name="type_selector" value="lines" /> <param name="pos_score_in_bin" value="block" /> <param name="plot_horizontal_lines" value="true" /> <param name="show_data" value="true" /> </conditional> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="bedgraph_matrix_track_option" /> <param name="track_input_bedgraph_matrix" value="tad_score.gz" ftype="bedgraph" /> <param name="title" value="TAD separation score (Ramirez et al.)" /> <param name="height_bedgraph" value="10" /> <conditional name="type"> <param name="type_selector" value="lines" /> <param name="pos_score_in_bin" value="center" /> <param name="plot_horizontal_lines" value="false" /> </conditional> </conditional> </repeat> <param name="image_file_format" value="png" /> <output name="outFileName" file="test_TADs_bdgm.png" ftype="png" compare="sim_size" delta="100" /> </test> <!--test 12--> <test> <param name="region" value="chrX:3000000-3300000"/> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="xaxis_option" /> <param name="xaxis_where" value="top" /> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="hic_matrix_option" /> <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/> <param name="title" value="Kc DpnII (Li et al. 2015)" /> <param name="colormap" value="Purples" /> <param name="depth" value="190000" /> <param name="transform" value="no" /> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="link_track_option" /> <param name="track_input_link" value="test.arcs" ftype="bed" /> <param name="title" value="" /> <param name="line_width" value="10" /> <param name="links_type" value="loops" /> <conditional name="color_link"> <param name="color_link_select" value="manually" /> <param name="color" value="red" /> </conditional> <param name="overlay_select" value="share-y" /> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="link_track_option" /> <param name="track_input_link" value="test.arcs" ftype="bed" /> <param name="title" value="" /> <param name="height" value="5" /> <conditional name="color_link"> <param name="color_link_select" value="colormap" /> <param name="color" value="hot" /> </conditional> <param name="max_value" value="5"/> <param name="invert_orientation" value="true" /> </conditional> </repeat> <param name="image_file_format" value="png" /> <output name="outFileName" file="test_link.png" ftype="png" compare="sim_size" delta="100" /> </test> <!--test 13--> <test> <param name="region" value="chrX:3000000-3300000"/> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="link_track_option" /> <param name="track_input_link" value="test.arcs" ftype="bed" /> <param name="title" value="default" /> <conditional name="color_link"> <param name="color_link_select" value="manually" /> <param name="color" value="#000000" /> </conditional> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="link_track_option" /> <param name="track_input_link" value="test.arcs" ftype="bed" /> <param name="title" value="ylim 20kb" /> <conditional name="color_link"> <param name="color_link_select" value="manually" /> <param name="color" value="#000000" /> </conditional> <param name="ylim" value="20000" /> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="link_track_option" /> <param name="track_input_link" value="test.arcs" ftype="bed" /> <param name="title" value="compacted" /> <conditional name="color_link"> <param name="color_link_select" value="manually" /> <param name="color" value="#000000" /> </conditional> <param name="compact_arcs_level" value="1" /> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="link_track_option" /> <param name="track_input_link" value="test.arcs" ftype="bed" /> <param name="title" value="highly compacted" /> <conditional name="color_link"> <param name="color_link_select" value="manually" /> <param name="color" value="#000000" /> </conditional> <param name="compact_arcs_level" value="2" /> </conditional> </repeat> <param name="image_file_format" value="png" /> <output name="outFileName" file="test_link2.png" ftype="png" compare="sim_size" delta="100" /> </test> <!--test 14--> <test> <param name="region" value="chrX:3000000-3300000"/> <section name="global_args"> <param name="title" value="Scale bar"/> <param name="trackLabelFraction" value="0.5"/> <param name="trackLabelHAlign" value="center"/> </section> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="spacer_option" /> <param name="spacer_height" value="1.0" /> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="scale_bar_option" /> <param name="title" value="default" /> <param name="spacer_height" value="1"/> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="scale_bar_option" /> <param name="title" value="scalebar where = right x_center = 3200000 size = 100002 fontsize = 8 line_width =2 color = red alpha = 0.5" /> <param name="color" value="red"/> <param name="alpha" value="0.5"/> <param name="line_width" value="2"/> <section name="scalebar_pos"> <param name="x_center" value="3200000"/> <param name="size" value="100002"/> </section> <param name="sb_where" value="right"/> <param name="fontsize" value="8"/> <param name="spacer_height" value="4"/> </conditional> </repeat> <param name="image_file_format" value="png" /> <output name="outFileName" file="test_scale_bar.png" ftype="png" compare="sim_size" delta="100" /> </test> <!--test 15--> <test> <param name="region" value="chrX:3300000-3500000"/> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="xaxis_option" /> <param name="xaxis_where" value="bottom" /> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="gene_track_option" /> <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" /> <param name="title" value="flybase" /> <param name="height_bed" value="10" /> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="gene_track_option" /> <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" /> <param name="title" value="UCSC" /> <param name="height_bed" value="10" /> <conditional name="bed_style"> <param name="bed_style_select" value="UCSC"/> <section name="bed_advanced"> <param name="arrow_interval" value="10"/> </section> </conditional> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="gene_track_option" /> <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" /> <param name="title" value="tssarrow" /> <param name="height_bed" value="10" /> <conditional name="bed_style"> <param name="bed_style_select" value="tssarrow"/> </conditional> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="gene_track_option" /> <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" /> <param name="title" value="tssarrow 5kb" /> <param name="height_bed" value="10" /> <conditional name="bed_style"> <param name="bed_style_select" value="tssarrow"/> <section name="bed_advanced"> <param name="arrow_length" value="5000"/> </section> </conditional> </conditional> </repeat> <param name="image_file_format" value="png" /> <output name="outFileName" file="test_tssarrow.png" ftype="png" compare="sim_size" delta="100" /> </test> <!--test 16--> <test> <param name="region" value="X:2700000-3100000"/> <section name="global_args"> <param name="decreasingXAxis" value="true"/> </section> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="bigwig_track_option" /> <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" /> <param name="title" value="(bigwig color=blue 2000 bins) overlayed with (bigwig mean color=red alpha = 0.5 max over 300 bins)" /> <param name="height_bigwig" value="7" /> <param name="color" value="#00b0f0" /> <section name="reading_bw_conditional"> <param name="number_of_bins" value="2000"/> </section> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="bigwig_track_option" /> <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" /> <param name="title" value="" /> <param name="color" value="#ff0000" /> <param name="alpha" value="0.5" /> <param name="summary_method" value="max" /> <section name="reading_bw_conditional"> <param name="number_of_bins" value="300"/> </section> <param name="overlay_select" value="share-y"/> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="xaxis_option" /> <param name="xaxis_where" value="bottom" /> </conditional> </repeat> <param name="image_file_format" value="png" /> <output name="outFileName" file="test_alpha_dec.png" ftype="png" compare="sim_size" delta="1000" /> </test> <!--test 17--> <test> <param name="region" value="chr2:73,800,000-75,744,000"/> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="bedgraph_track_option" /> <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" /> <param name="title" value="bedgraph color = blue transform = no" /> <param name="height_bedgraph" value="5" /> <param name="color" value="blue" /> <param name="show_data" value="true" /> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="bedgraph_track_option" /> <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" /> <param name="title" value="bedgraph color = blue transform = log" /> <param name="height_bedgraph" value="5" /> <param name="color" value="blue" /> <conditional name="logScale_conditional"> <param name="transform_selector" value="log"/> </conditional> <param name="show_data" value="true" /> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="bedgraph_track_option" /> <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" /> <param name="title" value="bedgraph color = red transform = log min_value = 1" /> <param name="height_bedgraph" value="5" /> <param name="color" value="red" /> <conditional name="logScale_conditional"> <param name="transform_selector" value="log"/> </conditional> <param name="min_value" value="1" /> <param name="show_data" value="true" /> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="bedgraph_track_option" /> <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" /> <param name="title" value="bedgraph color = green transform = log log_pseudocount = 2 min_value = 0" /> <param name="height_bedgraph" value="5" /> <param name="color" value="green" /> <conditional name="logScale_conditional"> <param name="transform_selector" value="log"/> <param name="log_pseudocount" value="2"/> </conditional> <param name="min_value" value="0" /> <param name="show_data" value="true" /> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="bedgraph_track_option" /> <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" /> <param name="title" value="bedgraph color = green operation = log(2+file) min_value = 0.7" /> <param name="height_bedgraph" value="5" /> <param name="color" value="green" /> <section name="op"> <param name="operation" value="log(2+file)" /> </section> <param name="min_value" value="0.7" /> <param name="show_data" value="true" /> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="bedgraph_track_option" /> <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" /> <param name="title" value="bedgraph color = black transform = log2 log_pseudocount = 1 min_value = 0" /> <param name="height_bedgraph" value="5" /> <param name="color" value="black" /> <conditional name="logScale_conditional"> <param name="transform_selector" value="log2"/> <param name="log_pseudocount" value="1"/> </conditional> <param name="min_value" value="0" /> <param name="show_data" value="true" /> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="bedgraph_track_option" /> <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" /> <param name="title" value="bedgraph color = black operation = log2(1+file) min_value = 0" /> <param name="height_bedgraph" value="5" /> <param name="color" value="black" /> <section name="op"> <param name="operation" value="log2(1+file)" /> </section> <param name="min_value" value="0" /> <param name="show_data" value="true" /> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="bedgraph_track_option" /> <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" /> <param name="title" value="bedgraph color = black transform = log2 log_pseudocount = 1 min_value = 0 y_axis_values = original" /> <param name="height_bedgraph" value="5" /> <param name="color" value="black" /> <conditional name="logScale_conditional"> <param name="transform_selector" value="log2"/> <param name="log_pseudocount" value="1"/> <param name="y_axis_values" value="original"/> </conditional> <param name="min_value" value="0" /> <param name="show_data" value="true" /> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="xaxis_option" /> <param name="xaxis_where" value="bottom" /> </conditional> </repeat> <param name="image_file_format" value="png" /> <output name="outFileName" file="test_log.png" ftype="png" compare="sim_size" delta="100" /> </test> <!--test 18--> <test> <param name="region" value="chrX:2700000-3100000"/> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="xaxis_option" /> <param name="xaxis_where" value="top" /> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="bedgraph_track_option" /> <param name="track_input_bedgraph" value="bedgraph_chrx_2e6_5e6.bg" ftype="bedgraph" /> <param name="title" value="file summary_method = mean number_of_bins=20" /> <param name="height_bedgraph" value="4" /> <param name="color" value="blue" /> <param name="show_data" value="true" /> <section name="reading_bdg_as_bw" > <param name="summary_method" value="mean" /> <param name="number_of_bins" value="20" /> </section> <param name="min_value" value="0" /> <param name="max_value" value="30" /> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="bedgraph_track_option" /> <param name="track_input_bedgraph" value="bedgraph2_X_2.5e6_3.5e6.bdg" ftype="bedgraph" /> <param name="title" value="second_file summary_method = mean" /> <param name="height_bedgraph" value="4" /> <param name="color" value="red" /> <param name="show_data" value="true" /> <section name="reading_bdg_as_bw" > <param name="summary_method" value="mean" /> </section> <param name="min_value" value="0" /> <param name="max_value" value="30" /> <param name="spacer_height" value="0.5" /> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="bedgraph_track_option" /> <param name="track_input_bedgraph" value="bedgraph_chrx_2e6_5e6.bg" ftype="bedgraph" /> <param name="title" value="operation = log1p(file) (no summary_method)" /> <param name="height_bedgraph" value="4" /> <param name="color" value="blue" /> <param name="show_data" value="true" /> <section name="op"> <param name="operation" value="log1p(file)" /> </section> <param name="spacer_height" value="0.5" /> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="bedgraph_track_option" /> <param name="track_input_bedgraph" value="bedgraph_chrx_2e6_5e6.bg" ftype="bedgraph" /> <param name="title" value="operation = file - second_file" /> <param name="height_bedgraph" value="8" /> <param name="color" value="blue" /> <param name="show_data" value="true" /> <conditional name="color_negative"> <param name="color_negative_select" value="true" /> <param name="color" value="red" /> </conditional> <section name="op"> <param name="operation" value="file - second_file" /> <param name="second_file" value="bedgraph2_X_2.5e6_3.5e6.bdg" ftype="bedgraph" /> </section> <param name="min_value" value="-30" /> <param name="max_value" value="30" /> </conditional> </repeat> <param name="image_file_format" value="png" /> <output name="outFileName" file="test_operation.png" ftype="png" compare="sim_size" delta="100" /> </test> <!--test 19--> <test> <param name="region" value="chr2:73,800,000-75,744,000"/> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="bedgraph_track_option" /> <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" /> <param name="title" value="bedgraph color = blue transform = no" /> <param name="height_bedgraph" value="5" /> <param name="color" value="blue" /> <param name="show_data" value="true" /> <param name="grid" value="true" /> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="bedgraph_track_option" /> <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" /> <param name="title" value="bedgraph color = blue transform = log" /> <param name="height_bedgraph" value="5" /> <param name="color" value="blue" /> <conditional name="logScale_conditional"> <param name="transform_selector" value="log"/> </conditional> <param name="show_data" value="true" /> <param name="grid" value="true" /> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="bedgraph_track_option" /> <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" /> <param name="title" value="bedgraph color = red transform = log min_value = 1" /> <param name="height_bedgraph" value="5" /> <param name="color" value="red" /> <conditional name="logScale_conditional"> <param name="transform_selector" value="log"/> </conditional> <param name="min_value" value="1" /> <param name="show_data" value="true" /> <param name="grid" value="true" /> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="bedgraph_track_option" /> <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" /> <param name="title" value="bedgraph color = green transform = log log_pseudocount = 2 min_value = 0" /> <param name="height_bedgraph" value="5" /> <param name="color" value="green" /> <conditional name="logScale_conditional"> <param name="transform_selector" value="log"/> <param name="log_pseudocount" value="2"/> </conditional> <param name="min_value" value="0" /> <param name="show_data" value="true" /> <param name="grid" value="true" /> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="bedgraph_track_option" /> <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" /> <param name="title" value="bedgraph color = green operation = log(2+file) min_value = 0.7" /> <param name="height_bedgraph" value="5" /> <param name="color" value="green" /> <section name="op"> <param name="operation" value="log(2+file)" /> </section> <param name="min_value" value="0.7" /> <param name="show_data" value="true" /> <param name="grid" value="true" /> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="bedgraph_track_option" /> <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" /> <param name="title" value="bedgraph color = black transform = log2 log_pseudocount = 1 min_value = 0" /> <param name="height_bedgraph" value="5" /> <param name="color" value="black" /> <conditional name="logScale_conditional"> <param name="transform_selector" value="log2"/> <param name="log_pseudocount" value="1"/> </conditional> <param name="min_value" value="0" /> <param name="show_data" value="true" /> <param name="grid" value="true" /> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="bedgraph_track_option" /> <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" /> <param name="title" value="bedgraph color = black operation = log2(1+file) min_value = 0" /> <param name="height_bedgraph" value="5" /> <param name="color" value="black" /> <section name="op"> <param name="operation" value="log2(1+file)" /> </section> <param name="min_value" value="0" /> <param name="show_data" value="true" /> <param name="grid" value="true" /> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="bedgraph_track_option" /> <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" /> <param name="title" value="bedgraph color = black transform = log2 log_pseudocount = 1 min_value = 0 y_axis_values = original" /> <param name="height_bedgraph" value="5" /> <param name="color" value="black" /> <conditional name="logScale_conditional"> <param name="transform_selector" value="log2"/> <param name="log_pseudocount" value="1"/> <param name="y_axis_values" value="original"/> </conditional> <param name="min_value" value="0" /> <param name="show_data" value="true" /> <param name="grid" value="true" /> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="xaxis_option" /> <param name="xaxis_where" value="bottom" /> </conditional> </repeat> <param name="image_file_format" value="png" /> <output name="outFileName" file="test_log_grid.png" ftype="png" compare="sim_size" delta="100" /> </test> <!--test 20--> <test> <param name="region" value="chrX:3000000-3300000"/> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="xaxis_option" /> <param name="xaxis_where" value="top" /> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="spacer_option" /> <param name="spacer_height" value="0.05" /> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="hic_matrix_option" /> <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/> <param name="title" value="depth = 300000; transform = log1p; min_value = 5 (next track: overlay_previous = share-y links_type = loops)" /> <param name="depth" value="300000" /> <param name="transform" value="log1p" /> <param name="min_value" value="5" /> <param name="show_masked_bins" value="false" /> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="link_track_option" /> <param name="track_input_link" value="test_wide.arcs" ftype="bed" /> <conditional name="color_link"> <param name="color" value="red" /> </conditional> <param name="line_width" value="5" /> <param name="links_type" value="loops" /> <param name="overlay_select" value="share-y" /> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="link_track_option" /> <param name="track_input_link" value="test_wide.arcs" ftype="bed" /> <conditional name="color_link"> <param name="color" value="RdYlGn" /> </conditional> <param name="line_width" value="3" /> <param name="invert_orientation" value="true" /> <param name="title" value="links line_width = 3 color RdYlGn" /> <param name="height" value="3" /> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="spacer_option" /> <param name="spacer_height" value="1" /> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="hic_matrix_option" /> <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/> <param name="title" value="depth = 300000; transform = log1p; min_value = 5 (next track: overlay_previous = share-y links_type = loops)" /> <param name="depth" value="300000" /> <param name="transform" value="log1p" /> <param name="min_value" value="5" /> <param name="show_masked_bins" value="false" /> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="link_track_option" /> <param name="track_input_link" value="test_wide.arcs" ftype="bed" /> <conditional name="color_link"> <param name="color" value="red" /> </conditional> <param name="line_width" value="5" /> <param name="links_type" value="loops" /> <param name="overlay_select" value="share-y" /> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="link_track_option" /> <param name="track_input_link" value="test_wide.arcs" ftype="bed" /> <conditional name="color_link"> <param name="color" value="RdYlGn" /> </conditional> <param name="line_width" value="3" /> <param name="invert_orientation" value="true" /> <param name="use_middle" value="true" /> <param name="title" value="links line_width = 3 color RdYlGn use_middle = true" /> <param name="height" value="3" /> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="vlines_track_option" /> <param name="track_input_bed_single" value="tad_classification.bed" ftype="bed" /> <param name="line_width" value="3" /> </conditional> </repeat> <param name="image_file_format" value="png" /> <output name="outFileName" file="test_arcs_use_middle.png" ftype="png" compare="sim_size" delta="1200" /> </test> <!--test 21--> <test> <param name="region" value="X:3000000-3600000"/> <section name="global_args"> <param name="trackLabelFraction" value="0.3"/> <param name="plotWidth" value="12"/> <param name="dpi" value="20"/> </section> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="scale_bar_option" /> <param name="title" value="scalebar where = right" /> <param name="where" value="right" /> <param name="spacer_height" value="0.5"/> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="scale_bar_option" /> <param name="title" value="scalebar scalebar_start_position = 3200000" /> <section name="scalebar_pos"> <param name="scalebar_start_position" value="3200000"/> </section> <param name="spacer_height" value="0.5"/> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="scale_bar_option" /> <param name="title" value="scalebar scalebar_start_position = 3200000 scalebar_end_position = 3250000" /> <section name="scalebar_pos"> <param name="scalebar_start_position" value="3200000"/> <param name="scalebar_start_position" value="3250000"/> </section> <param name="spacer_height" value="0.5"/> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="scale_bar_option" /> <param name="title" value="scalebar scalebar_start_position = 3200000 x_center = 3250000" /> <section name="scalebar_pos"> <param name="scalebar_start_position" value="3200000"/> <param name="x_center" value="3250000"/> </section> <param name="spacer_height" value="0.5"/> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="scale_bar_option" /> <param name="title" value="scalebar scalebar_start_position = 3200000 size = 50000" /> <section name="scalebar_pos"> <param name="scalebar_start_position" value="3200000"/> <param name="size" value="50000"/> </section> <param name="spacer_height" value="0.5"/> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="scale_bar_option" /> <param name="title" value="scalebar scalebar_end_position = 3200000 size = 50000" /> <section name="scalebar_pos"> <param name="scalebar_end_position" value="3200000"/> <param name="size" value="50000"/> </section> <param name="spacer_height" value="0.5"/> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="xaxis_option" /> <param name="xaxis_where" value="bottom" /> </conditional> </repeat> <param name="image_file_format" value="png" /> <output name="outFileName" file="master_scale_bar_startend.png" ftype="png" compare="sim_size" delta="100" /> </test> </tests> <help><![CDATA[ pyGenomeTracks ============== **pyGenomeTracks** is a visualization tool which aims to produce high-quality genome browser tracks that are highly customizable. Currently, it is possible to plot: - bigwig - bed/gtf (many options) - bedgraph - epilogos - narrow peaks - links - Hi-C matrices (cool or HiCExplorer h5) _________________ Usage ----- This tool takes various types of tracks as input: - **Hi-C tracks:** - **TAD vizualisation:** corrected Hi-C contact matrix to plot a contact heatmap. It is recommended to follow HiCExplorer's ``hicPlotMatrix`` instructions. Boundaries file can used, which is the output of HiCExplorer's ``hicFindTADs`` in bed format. If selected, TADs will be drawn directly on the contact heatmap. - **TAD score:** display TAD seperation score computed by HiCExplorer's ``hicFindTADs``. - **Chromatin states:** display blocks of different colors following a bed file. - **Gene track / Bed Track:** display genes or annotations in bed/gtf files. Labels like gene names can be toggled on or off. - **Link track:** display links (pair of coordinates) as arcs, triangles or loops. - **NarrowPeak track:** display narrowPeak (encode format) as boxes or as curve (reconstructed peak). - **Bigwig track:** generic bigwig track plotting. - **Bedgraph track:** generic bedgraph track plotting. - **Bedgraph matrix track** is used to specifically plot bm files computed by HiCExplorer's ``hicFindTADs`` (TAD seperation scores). - **Vlines:** vertical lines drawn on top of all tracks following a bed file. It is used as a visual support where regions start / end over all tracks, for example to display TAD boundaries computed by HiCExplorer's ``hicFindTADs``. - **Hlines:** horizontal lines drawn either by themselves or on top of other tracks. - **Spacer:** Add some space between two tracks. - **X-axis:** Plot x-axis scale wherever you want. - **Scale bar track:** Plot scale bar. For each track, parameters for the color, the width or the font size can be defined. _________________ Output ------ **pyGenomeTracks** output is similar to a genome browser screen-shot that besides the usual genes, and score data (like bigwig or bedgraph files) may also contains Hi-C data. The plot is composed of tracks that need to be specified. Below is represented the 85 Mb to 110 Mb region from human chromosome 2 visualized using **pyGenomeTracks**. TADs were computed by HiCExplorer's ``hicFindTADs``. The additional tracks added correspond to: TAD-separation score (as reported by HiCExplorer's ``hicFindTADs``), chromatin states, principal component 1 (A/B compartment) computed using HiCExplorer's ``hicPCA``, ChIP-seq coverage for the H3K27ac mark, DNA methylation, and a gene track. Data are from mouse cardiac myocytes, published by `Nothjunge et al. (2017)`_. .. image:: $PATH_TO_IMAGES/pyGenomeTracks.png :width: 70 % _________________ | For more information about pyGenomeTracks please consider our documentation on readthedocs_ or github_ .. _readthedocs: https://pygenometracks.readthedocs.io .. _github: https://github.com/deeptools/pyGenomeTracks .. _`Nothjunge et al. (2017)`: https://www.nature.com/articles/s41467-017-01724-9 ]]></help> <expand macro="citations" /> </tool>